[BioC] Affy Bioconductor with Rat230_2 chips

[Crispin Miller]

Hi Kim,
The new version of simpleaffy has a lot of bug fixes and stuff in it, so
I'd suggest using it anyway... ;-) 

The qc.stats code needs to know which chip you're using, to pick the
right spike probes - and detection p-value stuff needs to use it to work
out which alpha1 and alpha2 parameters to use...
I'm going to modify the code so you can specify the probes you wish to
use and stuff like that. In the next day or two I'll add the rat2302cdf
to the lists and upload a new version...
Cheers,
Crispin


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Kim Gernert
Sent: 23 April 2004 20:35
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Affy Bioconductor with Rat230_2 chips



I am trying to process Affymetrix array data from the new rat chip
(RAT230_2). We followed the vignette on setting up the new rat230-2.cdf
file and all seemed 
fine  (readaffy, rnadeg..., rma, etc.)  until I tried

(simpleaffy)  qc.stats

ERROR: I am sorry I donot know spike probes on rat230.2.cdf


Do I need the new simpleaffy (last download Mar 2004), do I need the new
R (currently running 1.8.1, on Linux)? or is there an additional script
I need to run to inform R of the new parameters 
(spikes, etc.) for the RAT230_2?


Your help is appreciated.

Kim M. Gernert




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